I don't know if this is any help to you or not, but in the collection of the California State Capitol Museum are many flags from many California regiments that served in New Mexico during the Civil War. Let me know if you would like more specifics about the flags of units that served in New Mexico.

By the way, one of my own ancestors served in New Mexico during the Civil War, and here is a link to a short biography I wrote about him. I hope you enjoy it!

http://suvcw.org/svr/forms/sixnews.pdf#page=4

-Sebastian Nelson
sebnelson@gmail.com